Ludovic Vallier

Mechanical signalling through collagen I regulates cholangiocyte specification and tubulogenesis during liver development

This study shows that collagen I mechanical signaling in synthetic hydrogels promotes cholangiocyte differentiation and bile duct formation from hiPSCs.

Genetic control couples TGFβ-independent pluripotent stem cell renewal to deterministic forward programming across germ layers

This paper introduces GERALT, a genetic circuit that enables TGFβ-independent hiPSC renewal and inducible lineage programming, improving differentiation efficiency and reducing medium complexity.

HLiCA: An integrated cell atlas of the healthy human liver

The paper integrates multiple datasets to create a comprehensive human liver cell atlas, identifying new cell types and associations with demographic factors.

Unveiling Gene Regulatory Network Dynamics using Fuzzy Clustering

The paper introduces Flufftail, a framework for fuzzy clustering in single-cell data, to infer gene regulatory network dynamics by leveraging membership probabilities and regulatory hub genes.

Both terminal misfolding and polymerisation contribute to disease-relevant phenotypic changes in cell models of alpha-1-antitrypsin deficiency-associated liver disease

This study shows that both terminal misfolding and polymerisation of Z 1-antitrypsin contribute to liver disease phenotypes, with terminal misfolding driving pro-fibrotic responses and metabolic changes.

NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation

This study shows NGN3 protein oscillations control timing of human pancreatic endocrine differentiation, not fate, through fold-change detection via an incoherent feedforward motif.

Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

This study creates a single-cell atlas of human liver development, identifying pathways and factors that guide hepatic cell fates and improving hepatocyte-like cell functionality.

Generation of functional hepatocytes by forward programming with nuclear receptors

This study generates functional hepatocytes from human pluripotent stem cells using forward programming with nuclear receptors, bypassing the limitations of traditional differentiation methods.

A spatially resolved single cell atlas of human gastrulation

This paper presents a spatially resolved single-cell transcriptome atlas of human gastrulation, identifying novel cell types and revealing key differences from mouse gastrulation.

Analysis of Endothelial-to-Haematopoietic Transition at the Single Cell Level identifies Cell Cycle Regulation as a Driver of Differentiation

This study identifies cell cycle regulation as a driver of endothelial-to-haematopoietic transition using single-cell transcriptomics in a human pluripotent stem cell system.

Single-cell RNA-seq of differentiating iPS cells reveals dynamic genetic effects on gene expression

The paper uses single-cell RNA-seq of differentiating iPS cells from 125 donors to identify expression quantitative trait loci influencing gene expression during endoderm differentiation.

Cell cycle regulators control mesoderm specification in human pluripotent stem cells

This study investigates how cell cycle regulators influence mesoderm specification in human pluripotent stem cells, finding that CDKs and pRb phosphorylation are context-dependent for efficient mesoderm formation.

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

The paper uses single-cell profiling of expression and DNA methylation to study splicing regulation and heterogeneity in human induced pluripotent stem cells.

Common genetic variation drives molecular heterogeneity in human iPSCs

This study analyzes 522 human iPSCs to identify genetic sources of phenotypic variation, finding 5-25% of variation in traits like differentiation capacity is due to individual differences.